7MKO

Escherichia coli RNA polymerase elongation complex

Summary for 7MKO

• Entry DOI: 10.2210/pdb7mko/pdb
• EMDB information: 23901
• Descriptor: DNA-directed RNA polymerase subunit alpha, 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, DNA-directed RNA polymerase subunit beta, ... (10 entities in total)
• Functional Keywords: rnap recycling, rapa, post-termination complex, ptc, transcription, transcription-dna-rna complex, transcription/dna/rna
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 8
• Total formula weight: 386049.40

Authors

Qayyum, M.Z.,Murakami, K.S. (deposition date: 2021-04-26, release date: 2021-06-02, Last modification date: 2024-05-29)

Primary citation

Qayyum, M.Z.,Molodtsov, V.,Renda, A.,Murakami, K.S.
Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli.
J.Biol.Chem., 297:101404-101404, 2021

PubMed Abstract: After transcription termination, cellular RNA polymerases (RNAPs) are occasionally trapped on DNA, impounded in an undefined post-termination complex (PTC), limiting the free RNAP pool and subsequently leading to inefficient transcription. In Escherichia coli, a Swi2/Snf2 family of ATPase called RapA is known to be involved in countering such inefficiency through RNAP recycling; however, the precise mechanism of this recycling is unclear. To better understand its mechanism, here we determined the structures of two sets of E. coli RapA-RNAP complexes, along with the RNAP core enzyme and the elongation complex, using cryo-EM. These structures revealed the large conformational changes of RNAP and RapA upon their association that has been implicated in the hindrance of PTC formation. Our results along with DNA-binding assays reveal that although RapA binds RNAP away from the DNA-binding main channel, its binding can allosterically close the RNAP clamp, thereby preventing its nonspecific DNA binding and PTC formation. Taken together, we propose that RapA acts as a guardian of RNAP by which RapA prevents nonspecific DNA binding of RNAP without affecting the binding of promoter DNA recognition σ factor, thereby enhancing RNAP recycling.

PubMed: 34774797
DOI: 10.1016/j.jbc.2021.101404

Experimental method

ELECTRON MICROSCOPY (3.15 Å)